Find best overlap threshold for EnrichMap
mem_find_overlap(
mem,
overlap_range = c(0.1, 0.99),
overlap_count = 2,
node_fraction = 0.5,
max_cutoff = 0.4,
debug = FALSE,
...
)list output from multiEnrichMap()
numeric range of Jaccard overlap values
numeric value passed to mem_multienrichplot()
which is used to filter the multienrichmap by Jaccard overlap
and by overlap_count.
numeric value between 0 and 1, to define the maximum fraction of nodes in the largest connected component, compared to the total number of non-singlet nodes.
logical indicating whether to return full debug data, which is used internally to determine the best overlap cutoff to use.
This function implements a straightforward approach to determine
a reasonable Jaccard overlap threshold for EnrichMap data.
It finds the overlap threshold at which the first connected
component is no more than max_cutoff fraction of the whole
network. This fraction is defined as the number of nodes in the
largest connected component, divided by the total number of
non-singlet nodes. When all nodes are connected, this fraction == 1.
We found empirically that a max_cutoff=0.4, the point at which the
largest connected component contains no more than 40% of all nodes,
seems to be a reasonably good place to start.
Other jam utility functions:
avg_angles(),
avg_colors_by_list(),
call_fn_ellipsis_deprecated(),
cell_fun_bivariate(),
collapse_mem_clusters(),
colorRamp2D(),
deconcat_df2(),
display_colorRamp2D(),
enrichList2geneHitList(),
filter_mem_genes(),
filter_mem_sets(),
find_colname(),
get_hull_data(),
get_igraph_layout(),
gsubs_remove(),
handle_igraph_param_list(),
isColorBlank(),
make_legend_bivariate(),
make_point_hull(),
order_colors(),
rank_mem_clusters(),
rotate_coordinates(),
subgraph_jam(),
subset_mem(),
summarize_node_spacing(),
xyAngle()